the pan of my cj was just painted and I plan to put new carpet down. Is there anything I should put between the painted floorboard and the carpet? Maybe some type of sound deadening material (dynomat), herculiner, or pad?

Topless is right, carpet traps moisture and will rust out your floorboards in a heartbeat. I just replied to someone else about this, but you can develop mold spores that can make you pretty sick from a wet carpet with the top up on a hot day (this is from personal experience guys). have your tub rhino-lined and keep those drain plugs open. If you still can, RETURN that carpet!